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Doni Baskoro
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SciTech #ScienceSunday Digest - 51/2016.
Permalink here: http://www.scitechdigest.net/2016/12/writing-dna-macro-quantum-effects-deep.html

Writing DNA, Macro quantum effects, Autonomous drone advances, Deep learning music, Reversing stem cell development, Reversing animal aging, Photovoltaic atomic veins, Noninvasive mind control, Microfluidic blood sensors, Deep learning supercomputing.

1. Writing DNA with Twist
Twist Bioscience has developed a new silicon chip for writing and synthesising DNA sequences, taking the conventional 96 well approach producing one gene to a new architecture that produces 9,600 genes that makes DNA synthesis significantly faster and cheaper https://medium.com/@Hello_Tomorrow/is-dna-the-next-silicon-c88e6e89754d#.v26ntfksi. Combined with rapid, cheap DNA sequencing chips, rapid, cheap DNA synthesis chips will accelerate the transformation of biotechnology, allowing custom DNA sequences to be produced for quickly engineering organisms of interest.

2. Quantum Effects in Macro Materials
A new type of topological insulator (conductor on surface, insulator in bulk) made from bismuth and selenium, happens to slightly rotate and change a beam of terahertz light shone through the material http://www.sciencealert.com/this-new-material-might-show-the-link-between-classical-and-quantum-physics. This quantum effect is typically observed only at atomic scales and never in macro materials; it obeyed the same mathematics and is the first time such a quantum effect has been observed in large topological insulators. It is hoped that the link might allow further probing between quantum and classical mechanics.

3. Advances with Autonomous Drones
First, an optimal reciprocal collision avoidance strategy has been developed to allow large numbers of drones to fly through the same airspace, dynamically avoid colliding, and all while minimising g-forces for the purpose of future passenger-transport drones http://spectrum.ieee.org/automaton/robotics/drones/limiting-jerks-for-comfortable-commuting-by-personal-drone. Second, Amazon demonstrated its first autonomous drone product delivery https://www.amazon.com/b?node=8037720011. Finally, drones are being used for cheap but difficult environmental monitoring applications such as methane monitoring, an area we can expect to rapidly expand into drone monitoring of a great many things http://spectrum.ieee.org/energywise/energy/environment/drones-take-to-the-skies-to-screen-for-methane-emissions.

4. Deep Learning Music Composition
A new deep learning system called DeepBach was trained and validated against music composed by the composer Bach, and is able to produce new music in the same style as Bach to the extent of convincing humans about 50% of the time that they were actually written by Bach https://www.technologyreview.com/s/603137/deep-learning-machine-listens-to-bach-then-writes-its-own-music-in-the-same-style/. Interestingly the same humans only picked 75% of the compositions actually written by Bach. This marks another big step on the way of machines producing creative outputs and artworks, suggesting that future deep learning systems might produce novel music (or other works) in any particular artist’s style given some general starting parameters.

5. Reversing Human Embryonic Stem Cell Development
A mixture of three different chemical inhibitors has been demonstrated to further wind back the developmental clock of human embryonic stem cells, finally achieving the same long-hoped-for flexibility that researchers have enjoyed with embryonic stem cells from mice https://www.eurekalert.org/pub_releases/2016-12/jhm-rtb121416.php. These stem cells are now much easier to keep alive and the technique successfully reset 25 human stem cell lines, showed more malleable gene expression profiles, avoided abnormal DNA changes sometimes characterised by other techniques, and could be subsequently differentiated into vascular or neural cell types (for example) at double or triple the frequencies of conventional human embryonic stem cells. Meanwhile stem cells are being used to create and study amniotic sac formation http://ns.umich.edu/new/releases/24415-how-does-the-amniotic-sac-form-u-m-team-uses-stem-cells-to-study-earliest-stages.

6. Reversing Aging in Animals
In related work using conventional reprogramming techniques with four factors that turn cells into induced pluripotent stem cells, researchers demonstrated that administering these factors for short durations had rejuvenating, anti-aging effects https://www.salk.edu/news-release/turning-back-time-salk-scientists-reverse-signs-aging/. Skin cells showed reversal of aging hallmarks while remaining skin cells, mice with progeria looked younger with improved organ function and lived 30% longer, while normally aged mice had improved regenerative and healing capacity. As promising as this is it should be approached with caution due to a number of reasons outlined here https://www.fightaging.org/archives/2016/12/temporarily-applying-pluripotency-reprogramming-factors-to-adult-mice/. Meanwhile microRNA levels over time appear to correlate well with life span https://www.fightaging.org/archives/2016/12/microrna-differences-across-the-course-of-aging-correlate-with-life-span/.

7. Atomic Veins Boost Photovoltaic Performance
Adding a network of linear atomic defects by removing atoms on two-dimensional material surfaces such as molybdenum diselenide creates the equivalent of atom-thick wires that can channel electrons and light http://phys.org/news/2016-12-lines-atoms-thin-electronic-materials.html. Early stage research but offering promising avenues to boost photovoltaic performance and explore new properties on these surfaces that influence electrical and optical performance and both semi- and super-conductivity.

8. Noninvasive Mind Control of Robotic Hands
A new 64 electrode EEG system allows people to operate a robotic arm to reach and grasp objects using just their thoughts and without an invasive brain implant https://twin-cities.umn.edu/news-events/umn-research-shows-people-can-control-robotic-arm-their-minds. Studies with human volunteers required them to devote time with the system to learn to imagine moving their own arm, and the robotic arm, without actually moving their arm. In related news a soft prosthetic hand utilises stretchable optical waveguides to detect curvature, elongation, and force and designed to give robots and prosthetics a much better sense of touch http://mediarelations.cornell.edu/2016/12/12/new-robot-has-a-human-touch/.

9. Sensors & Microfluidics for Real-time Blood Monitoring
A microfluidic biosensor chip uses gold electrodes patterned with DNA aptamers to measure molecules of interest in real-time, significantly boosting the accuracy and frequency of measurements and solving other problems that an earlier prototype chip possessed http://spectrum.ieee.org/the-human-os/biomedical/devices/sensor-system-offers-realtime-control-of-drug-levels-in-blood. In one demonstration the concentration of a chemotherapy drug was monitored in rabbits in order to continuously dose the animal with precise amounts of the drug to maintain optimal therapeutic effect while minimising side effects. Different DNA aptamers can be engineered to capture just about any molecule (or combination) of interest, so this is a very interesting platform. In related news another microfluidic chip rapidly detects metastatic cancers cells in drops of blood https://www.wpi.edu/news/wpi-researchers-build-%E2%80%9Cliquid-biopsy%E2%80%9D-chip-detects-metastatic-cancer-cells-drop-blood.

10. Big & Small Supercomputing Initiatives
First, Cray announced the results of a deep learning supercomputing collaboration with Microsoft and the Swiss National Supercomputing Centre that runs larger deep learning models and significantly accelerating the deep learning training process, obtaining results in hours that previously might have taken weeks or months http://investors.cray.com/phoenix.zhtml?c=98390&p=irol-newsArticle&ID=2228098. Second, Nvidia’s DGX-1 supercomputer is a complete dedicated package for machine learning, the size of a briefcase and costing $129,000 that seems to be producing decent advances for ever-more customers https://www.technologyreview.com/s/603075/the-pint-sized-supercomputer-that-companies-are-scrambling-to-get/.

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SciTech #ScienceSunday Digest - 34/2016.
Permalink here: http://www.scitechdigest.net/2016/08/jumping-robot-legs-uber-launches.html

Purifying carbon nanotubes, Anti-inflammatories for Alzheimer’s, Jumping robot legs, Protein sweeteners, Fortified GMO rice, Uber launches autonomous cars, Bacterial conducting nanowires, Superconducting electron superfluids, CRISPR for EvoDevo, Massively engineered genomes.

1. Purifying Carbon Nanotubes
One of the biggest obstacles to developing carbon nanotube applications is separating mixtures of carbon nanotubes to obtain pure samples of either metallic or semiconducting nanotubes depending on the requirements of the application. A new method for doing this involves a newly engineered polymer based on a template that was able to wash away semiconducting carbon nanotubes to leave metallic versions for use, but is now able to selectively wash away metallic carbon nanotubes to leave semiconducting versions for use http://dailynews.mcmaster.ca/article/mcmaster-researchers-resolve-a-problem-that-has-been-holding-back-a-technological-revolution/. Next step will be to make more efficient polymers and scale up production.

2. Anti-Inflammatory Drugs Treat Alzheimer's
Recent work shows that certain types of common Non-Steroidal Anti-Inflammatory Drugs are effective in treating Alzheimer’s disease in animal models by completely reversing memory loss and brain inflammation http://www.manchester.ac.uk/discover/news/treatment-option-for-alzheimers-disease-possible. Next steps will be to confirm that the effect carries over to humans and, with these drugs already on the market for other NSAID-related indications, seek approval for repurposing in light of side effects.

3. Explosive Jumping Robot Legs
A new “GOAT” robot leg design is capable of explosive jumping to twice its height that can also walking, running, and compliant landings http://spectrum.ieee.org/automaton/robotics/robotics-hardware/goat-robot-leg-demonstrates-explosive-jumping. Next step is to improve the hardware then mount the legs onto both bipedal and quadruped robots, which I think will be very impressive to see. In related robotic automation news, agricultural fruit and vegetable picking robots continue to get better with the demonstration of a new automated apple picker http://spectrum.ieee.org/automaton/robotics/industrial-robots/sri-spin-off-abundant-robotics-developing-autonomous-apple-vacuum.

4. Protein-based Artificial Sweeteners
A protein that occurs naturally in a West African fruit turns out to be 2,000 sweeter than sugar http://phys.org/news/2016-08-protein-big-sweetener.html. Producing the protein at scale for commercial uses has been problematic however, although in this recent work the use of genetically engineered yeast to produce larger amounts of the protein via fermentation is showing promise. A reliable source of protein-based, non-sugar, non-aspartame sweeteners would benefit the food and beverage industry by circumventing the different problems surrounding conventional sweeteners.

5. Engineered Rice Addresses Zinc & Iron Deficiency
A new type of genetically engineered rice that fixes and stores significantly more zinc and iron has been created that can improve the lives of those suffering from deficiencies, especially in the third world http://www.nextbigfuture.com/2016/08/modified-rice-has-five-times-zinc-and.html. This is a similar approach to the Golden Rice that has been around for a while that was engineered to produce more Vitamin A. In this case the iron and zinc content of grains was increased from ~3ppm to 15ppm and from 16ppm to 45ppm respectively. Next steps are to introduce the rice for cultivation in Bangladesh.

6. Uber Introduces Autonomous Car Service
Uber and Volvo will introduce a driverless taxi service in Pittsburgh this month using a fleet of 100 Volvo vehicles http://spectrum.ieee.org/cars-that-think/transportation/self-driving/uber-will-start-driverless-service-in-pittsburghthis-month. This won’t be a general-purpose service, but will rather ferry passengers between fixed points of interest around the city and the collaboration will further develop technology and mapping resources. The cars will apparently include “safety drivers” in the cars for the first rollout, not only to intervene if necessary but also to condition customers to get comfortable with autonomous taxis.

7. Producing Conducting Nanowires with Bacteria
Genetically engineered bacteria can now be controllably harnessed to produce electrically conducting nanowires http://www.onr.navy.mil/Media-Center/Press-Releases/2016/Geobacter.aspx. This builds on earlier work that first discovered and characterised the natural bacterial nanowires, which allowed the rational design of modified nanowires by rearranging amino acids into an improved architecture. The nanowires produced by the bacteria are protein-based, 2,000 times more conductive than natural counterparts, and measured 1.5 nanometers wide. Future applications include electronics, sensors, and as power conductors in microbial circuits.

8. Electron Superfluid Critical for High Temperature Superconductivity
Recent analysis of materials that perform as high temperature superconductors reveals that their atomic architecture facilitates the formation of electron pairs into an electron superfluid that flows without resistance https://www.bnl.gov/newsroom/news.php?a=11864. Analysing different types of these copper oxide materials (that include lanthanum and strontium) showed that differences in transition temperature between materials are determined by differences in the density of electron pairs. This challenges conventional theories of superconductivity and is hoped that this better understanding will lead to the design of materials with much higher, room-temperature transition temperatures.

9. CRISPR Accelerating the Field of Evolutionary Developmental Biology
CRISPR is having a transformative effect on the field of evolutionary developmental biology by allowing experiments to not only be done that could never be contemplated before but by significantly accelerating the rate and progress of the field http://www.nature.com/news/crispr-s-hopeful-monsters-gene-editing-storms-evo-devo-labs-1.20449. Recent work traced the gene changes required for (i) turning fins into feet, (ii) improving photoreceptors in butterflies to detect a broader spectrum of colours, and (iii) how crustaceans acquired claws. Future work will look to modify the genes and pathways involved in building chicken beaks to find the sequences required for building theropod dinosaur snouts; we might yet get our chickenosaurus.

10. Most Engineered Bacterial Genome
The most engineered and radically rewritten bacterial genome has been produced recently http://www.nature.com/news/radically-rewritten-bacterial-genome-unveiled-1.20451. The synthetic genome was synthesised with 3.8% of the original genome edited to replace 7 of 64 codons with code that produces the same components and so create an organism that functions on 57 instead of 64 codons. This would not have been possible even a few years ago and represents the largest completely synthesised genome with the most functional changes; next step is to boot it up into a functional cell.

Bonus: Festo’s Fantastic Flying Robots.
The latest robots from Festo are always a pleasure to behold http://spectrum.ieee.org/video/robotics/robotics-hardware/festos-fantastical-flying-robots

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How big is a proton?

We thought we knew.  New measurements say we were 4% off.  That may not seem like much - but it's enough to be a serious problem!

We can measure the proton radius by bouncing electrons off it, or by carefully studying the energy levels of a hydrogen atom.  People have measured it many times, and the different measurements agree pretty well.  Here's the answer:

0.8775 ± 0.0051 femtometers   

A femtometer is 10 to the minus 15th meters, or a quadrilionth of a meter. 

But you can make a version of hydrogen with a muon replacing the electron.  The muon is the electron's big brother.  It's almost the same, but 207 times heavier.   So, muonic hydrogen is about 1/207 times as big across.  And that makes the effects of the proton radius easier to detect! 

So, in principle, we should be able measure the radius of a proton more accurately using muonic hydrogen. 

So that's what they did - in Switzerland, back in 2010.  They repeated the experiment in 2013.   Here's what they got:

0.84087 ± 0.00039 femtometers
 
In theory, this is about ten times more accurate.  However, it's way off from all the earlier measurements!  7 standard deviations off.

This story is in the news again today.  The same team just used muons to measure the radius of deuterium - a proton and a neutron stuck together.  And again, they're getting a different answer than what people get using electrons.

Could some new physics be responsible?  Some serious mistake in our theory of particles?   The guy who led the new experiment, Randolph Pohl, said:

“That would, of course, be fantastic.  But the most realistic thing is that it’s not new physics.”

I like that.  A good experimentalist does not  jump to dramatic conclusions.  Pohl guesses that we're wrong about the value of the Rydberg constant, a number that goes into calculating the proton mass from the experimental data. 

However, it's worth noting that there's another puzzle about muons. Electrons and muons are like tiny magnets.  When we calculate how strong the magnetic field of an electron is, we get results that match experiment incredibly well.  But when we do the same calculation for the muon, we're off by 3.4 standard deviations.

So maybe, just maybe, there's something funny going on with muons, which hints at new physics beyond the Standard Model.  I doubt it.  But you never know.  

Check out this for more:

https://www.quantamagazine.org/20160811-new-measurement-deepens-proton-radius-puzzle/

If our estimate of the Rydberg constant were 4 standard deviations off, that would do the job.  That sounds like a lot... but if you look at the graphs here, you'll see other cases when we were way off about things!

 For even more, check out this:

• Carl E. Carlson, The proton radius puzzle, https://arxiv.org/abs/1502.05314

#physics #protonRadiusPuzzle
#spnetwork arXiv:1502.05314
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